Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The RNA exosome contributes to gene expression regulation during stem cell differentiation [CAGE]

ABSTRACT: The RNA exosome contributes to gene expression regulation during stem cell differentiation [CAGE]

PROVIDER: PRJNA475879 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7300120.fastq.gz	Fastqsanger.gz
	SRR7300113.fastq.gz	Fastqsanger.gz
	SRR7300114.fastq.gz	Fastqsanger.gz
	SRR7300115.fastq.gz	Fastqsanger.gz
	SRR7300116.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

The RNA exosome contributes to gene expression regulation during stem cell differentiation [CAGE]

Project description:Gene expression programs change during cellular transitions. It is well established that a network of transcription factors and chromatin modifiers regulate RNA levels during embryonic stem cell (ESC) differentiation, but the full impact of post-transcriptional processes remains elusive. While cytoplasmic RNA turnover mechanisms have been implicated in differentiation, the contribution of nuclear RNA decay has not been investigated. Here, we differentiate mouse ESCs, depleted for the ribonucleolytic RNA exosome, into embryoid bodies to determine to which degree RNA abundance in the two states can be attributed to changes in transcription vs. RNA decay by the exosome. As a general observation, we find that exosome depletion mainly leads to the stabilization of RNAs from lowly transcribed loci, including several protein-coding genes. In particular, transcripts that are differentially expressed between states tend to be more exosome sensitive in the state where expression is low. We conclude that the RNA exosome contributes to down-regulation of transcripts with disparate expression, often in conjunction with transcriptional down-regulation.

2018-08-31 | GSE115710 | GEO

The RNA exosome contributes to gene expression regulation during stem cell differentiation [CAGE 2]

Project description:Gene expression programs change during cellular transitions. It is well established that a network of transcription factors and chromatin modifiers regulate RNA levels during embryonic stem cell (ESC) differentiation, but the full impact of post-transcriptional processes remains elusive. While cytoplasmic RNA turnover mechanisms have been implicated in differentiation, the contribution of nuclear RNA decay has not been investigated. Here, we differentiate mouse ESCs, depleted for the ribonucleolytic RNA exosome, into embryoid bodies to determine to which degree RNA abundance in the two states can be attributed to changes in transcription vs. RNA decay by the exosome. As a general observation, we find that exosome depletion mainly leads to the stabilization of RNAs from lowly transcribed loci, including several protein-coding genes. Depletion of the nuclear exosome cofactor RBM7 leads to similar effects. In particular, transcripts that are differentially expressed between states tend to be more exosome sensitive in the state where expression is low. We conclude that the RNA exosome contributes to down-regulation of transcripts with disparate expression, often in conjunction with transcriptional down-regulation.

2018-08-31 | GSE118043 | GEO

The RNA exosome contributes to gene expression regulation during stem cell differentiation [CAGE 2]

Project description:The RNA exosome contributes to gene expression regulation during stem cell differentiation [CAGE 2]

| PRJNA484178 | ENA

The RNA exosome contributes to gene expression regulation during stem cell differentiation [RNA-Seq]

2018-08-31 | GSE115714 | GEO

The RNA exosome contributes to gene expression regulation during stem cell differentiation [PRO-Seq]

2018-08-31 | GSE115713 | GEO

The RNA exosome contributes to gene expression regulation during stem cell differentiation [RNA-Seq 2]

Project description:Gene expression programs change during cellular transitions. It is well established that a network of transcription factors and chromatin modifiers regulate RNA levels during embryonic stem cell (ESC) differentiation, but the full impact of post-transcriptional processes remains elusive. While cytoplasmic RNA turnover mechanisms have been implicated in differentiation, the contribution of nuclear RNA decay has not been investigated. Here, we differentiate mouse ESCs, depleted for the ribonucleolytic RNA exosome, into embryoid bodies to determine to which degree RNA abundance in the two states can be attributed to changes in transcription vs. RNA decay by the exosome. As a general observation, we find that exosome depletion mainly leads to the stabilization of RNAs from lowly transcribed loci, including several protein-coding genes. Depletion of the nuclear exosome cofactor RBM7 leads to similar effects. In particular, transcripts that are differentially expressed between states tend to be more exosome sensitive in the state where expression is low. We conclude that the RNA exosome contributes to down-regulation of transcripts with disparate expression, often in conjunction with transcriptional down-regulation.

2018-08-31 | GSE118054 | GEO

The RNA exosome contributes to gene expression regulation during stem cell differentiation [PRO-Seq 2]

Project description:Gene expression programs change during cellular transitions. It is well established that a network of transcription factors and chromatin modifiers regulate RNA levels during embryonic stem cell (ESC) differentiation, but the full impact of post-transcriptional processes remains elusive. While cytoplasmic RNA turnover mechanisms have been implicated in differentiation, the contribution of nuclear RNA decay has not been investigated. Here, we differentiate mouse ESCs, depleted for the ribonucleolytic RNA exosome, into embryoid bodies to determine to which degree RNA abundance in the two states can be attributed to changes in transcription vs. RNA decay by the exosome. As a general observation, we find that exosome depletion mainly leads to the stabilization of RNAs from lowly transcribed loci, including several protein-coding genes. Depletion of the nuclear exosome cofactor RBM7 leads to similar effects. In particular, transcripts that are differentially expressed between states tend to be more exosome sensitive in the state where expression is low. We conclude that the RNA exosome contributes to down-regulation of transcripts with disparate expression, often in conjunction with transcriptional down-regulation.

2018-08-31 | GSE118052 | GEO

The RNA exosome contributes to gene expression regulation during stem cell differentiation

Project description:The RNA exosome contributes to gene expression regulation during stem cell differentiation

| PRJNA475875 | ENA

The RNA exosome contributes to gene expression regulation during stem cell differentiation [RNA-Seq]

Project description:The RNA exosome contributes to gene expression regulation during stem cell differentiation [RNA-Seq]

| PRJNA475880 | ENA

The RNA exosome contributes to gene expression regulation during stem cell differentiation [PRO-Seq]

Project description:The RNA exosome contributes to gene expression regulation during stem cell differentiation [PRO-Seq]

| PRJNA475881 | ENA